Integrated Data Repository Mike Conlon, PhD Associate Director, UF CTSI The UF CTSI is supported in...

The UF CTSI is supported in part by NIH awards UL1 TR000064, KL2 TR000065 and TL1 TR000066

Integrated Data Repository

Mike Conlon, PhDAssociate Director, UF CTSI


What if we had a repository …

• That contained clinical data from Epic for all patients in the health care system

• Combined that data with information regarding the patient’s willingness to participate in research

• Had information on labs, procedures, diagnoses, medications, biospecimens, genetic markers

• Had information over care events


How we’d like to have the answers

• Quickly – at our desks, interactive• Professionally – with full consideration of the

complexity of clinical data, translating our ideas into the details necessary for a an accurate result

• Securely –protecting patient privacy• Accurately• Across clinics and hospitals• Data available for analysis via appropriate

protocols, combined with additional research data


The 2008 PlanData integration lowers the barriers to using and more importantly, reusing data. By anticipating researcher needs building and operating interfaces between source systems and access for clinicians and researchers, we serve all goals of the CTSI: 1) barriers to interaction are reduced by providing data in easily accessible, standardized formats; 2) training programs are enhanced by providing access to substantial data resources; 3) access to advanced technologies is facilitated by making data from these systems available for analysis; and 4) new opportunities are created for collaboration by making standardized data available to all members of the CTSI across the state. Data integration work consists of collaborating with data source system providers and computational resource providers to develop data pathways leading to reusable, standardized formats available through access systems such as the CTSI Portal. CRU and TTRP source systems often must be integrated to intermediate computational resources for processing (Fig. 3). Molecular data and imaging data often require significant computation whose results must then be transformed into standard formats for access. Data format standards exist and are emerging across research and health informatics (83).

Once data are transformed they can then be organized for search and secured with access control standardized through IAM processes in an IDR. To integrate data in support of translational research we will adopt national standards for security, software and a data interchange (C.2.a), provide integration to emerging national repositories (C.2.b) and establish an enterprise architecture for informatics (C.2.c). The resulting integration of TTRP (C.2.d) and CRU (C.2.e) resources will result in integrated research database delivery (C.2.f). Using standardized access methods for data we will transform our practice of reusing data, thereby encouraging data reuse and sharing (C.2.g).

Integrated Data Repository



I2B2 Cohort Discovery

Patients 329,986Visits 1,786,999Procedures 9,957,757Diagnoses 12,388,053

Adding 600K procedures per month

IDR will double in size when Jacksonville is added in summer, 2013


Virtual Desktop Interface (VDI)• PHI from the IDR may be released to the

investigator– Under IRB approval– With a Data Use Agreement

• Data released from the IDR will be provided in a secure environment – a VDI that enable the investigator to analyze the data without having to move the data to insecure environments

• See http://vdi.ahc.ufl.edu to get started

http://vdi.ahc.ufl.edu/


IDR Timeline


IDR support and governance• The IDR is jointly sponsored by Shands and the

CTSI• The support team includes data modelers,

analysts, programmers, DBAs, ETL experts• A steering committee meets regularly to set

direction and monitor progress• For more information, please contact the IDR

project lead, Gigi Lipori ([email protected])


I2B2 Training and Sign on

• I2B2 training is available on-line at the IDR web site:– http://idr.ahc.ufl.edu/i2b2/i2b2-training-module/

• Once training is complete (10 minutes), you can apply for sign on to i2b2

• Once approved (next day), you can sign on to i2b2 at:– http://i2b2.idr.ahc.ufl.edu

http://idr.ahc.ufl.edu/i2b2/i2b2-training-module/

http://idr.ahc.ufl.edu/i2b2/i2b2-training-module/

http://i2b2.idr.ahc.ufl.edu/

http://i2b2.idr.ahc.ufl.edu/


Professional Services

• Professional services are available if your queries are complex, or you are unfamiliar with Shands clinical data, its coding and its nuances

• Professional services for developing cohorts and creating datasets is available at cost ($$)

• Contact Dr. Felix Liu ([email protected]) for an appointment regarding your IDR needs.

mailto:[email protected]

Consent2Share• Initiated on 9/11/12• Consent form given with admissions packet• Consent asks 2 questions

– Can we store your excess tissue with protected health information?

– Can we re-contact you for a future study? • Collected by admissions clerk, data entered into

EPIC, consent form scanned with other documents

• Patient’s physician can access pt response, answer questions

• Informed Consent Hotline to answer initial questions

• CTSI patient research advocate for more detailed queries


Results to date (>10,000)85% “yes” for samples79% “yes” for recontact


CTSI Biorepository• Biospecimen collection, processing and

storage. Stored biospecimens can be used by any researcher with IRB-approved protocols.

• Prospective biospecimen collection to fulfill investigator needs for IRB-approved protocols.

• Storage for biospecimens collected by investigators. Stored biospecimens belong solely to the investigator.

• Oversight of the release of biospecimens from the UF Department of Pathology for other IRB-approved research protocols.

• Pathology services including those provided by the Molecular Pathology Core and confirmation of diagnosis by a board-certified pathologist upon request.

One of two Hamilton Storage Technologies’ SAM -80°C automated sample management systems (Robotic freezers). The biorepository also has eight Forma Thermo Scientific -80°C Freezers with back-up CO2 and sensaphone alarm systems including back-up storage space, centrifuge for basic bodily fluid processing, QiaCube for small volume RNA, DNA and protein purification, Agilent Bioanalyzer for RNA, DNA and protein quality control analysis, OnCore BioSpecimen Management

Genetic Information from the UF & Shands Personalized Medicine Program

Challenge: genetic polymorphism of CYP2C19 leads to reduced ability to activate clopidogrel (Plavix) and increased risk of cardiovascular complication


For More Information

On the web: http://idr.ahc.ufl.edu


http://www.ctsi.ufl.edu/

Integrated Data Repository Mike Conlon, PhD Associate Director, UF CTSI The UF CTSI is supported in...

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